An experiment was conducted to examine the effect of estrus synchronization protocols and steroid hormones concentrations on somatic cell count (SCC) of transitional-anestrus local-Damascus cross goats' milk. Fifty-six goats (2-4-year old) were randomly assigned to three groups: fluorogestone acetate (FGA, n = 19), FGA-Prostaglandin (FGA-PGF, n = 19) and control (n = 18) groups. Intravaginal sponge containing 40 mg FGA was inserted for 13 days and an injection of 600 IU equine chorionic gonadotropin (eCG) was administered for goats of FGA and FGA-PGF groups at the time of sponge removal (day 0). In addition, goats of FGA-PGF group were injected with 10 mg dinoprost tromethamine (PGF2alpha) on day 0. Five fertile local-Damascus cross bucks were turned-in with all goats on day 0. Blood and milk samples were collected from all goats on days -13 (beginning of experiment), -6, 0, 1, 2, 7, 13 and 20 (end of the experiment). Four-year old and second-parity goats had significantly higher (p < 0.05) SCC of both udder halves than 2- and 3-year old and first-parity goats, respectively. There was a significant effect (p < 0.05) for treatment and number of kids born in the last kidding season on SCC of both udder halves. Neither estradiol nor progesterone concentrations were correlated with SCC in goats in this experiment. The SCC of both udder halves and left udder halves in goats of the control and FGA groups, respectively, increased significantly (p < 0.05) after sponge removal and buck introduction when compared with day 0, with no differences in the FGA-PGF group. This increase in SCC of the control and FGA groups coincided with peak estrus behavior. However, SCC was far below the upper limit of the current standard for normal milk. In conclusion, induction of estrus with progestagen based programs and buck introduction may cause temporary significant increase in SCC. However, the SCC values during this period of temporary increase were still in the range of acceptable values for normal milk. With the current standards for SCC of 1,000,000/ml as legal limit for abnormal milk control programs in goats, estrus synchronization programs and the estrus status should not be considered when bulk-tank milk SCC is being investigated.